Nucleic acid and Protein interaction network designer

Include
Minimum Length Maximum Length
Protein interaction with:
Distance Calculation Method
Similarity
({{Explorer.Criteria.Configuration.Sim}} %)
Distance Cutoff
Distance (Å)
Empty boxes consider all items.
UID PDB Sequence Len Description Score Local % Global %
{{pdb}} +{{rna.PDBs.length-4}} {{rna.sequence.substring(0, 10) + '...' + rna.sequence.substring(rna.sequence.length-10, rna.sequence.length)}}
{{rna.sequence}}
{{rna.sequence.length}}
{{rna.auth_desc.substring(0, 20)+' ...'}}
{{rna.auth_desc}}
{{rna.Score}} {{rna.globalSim.toFixed(2)}} {{rna.localSim.toFixed(2)}}
{{rna.auth_desc}}
Organisms

{{o}}

Sequence {{rna.sequence.length}} nucleotides

{{rna.sequence}}

PDB IDs {{rna.PDBs.length}} PDB chains

{{pdb}}

Similairty Alignemnt Index
UID Score Local Global (Identical) Start End
{{sim.uid1}} {{sim.uid2}} {{sim.score}} {{sim.LocalSimilarity.toFixed(2)}} % {{sim.GlobalSimilarity.toFixed(2)}} % {{sim.start}} {{sim.end}}
Atoms' count closer than thresholds in Angstrom(Å)
Protein #Complexes 2.0 2.5 3.0 3.4 3.7 4.0 5.0 7.0
{{mol.uid_pro}} {{mol.frequency}} {{mol.md20_mean.toFixed(1)}} ± {{mol.md20_std.toFixed(1)}} {{mol.md25_mean.toFixed(1)}} ± {{mol.md25_std.toFixed(1)}} {{mol.md30_mean.toFixed(1)}} ± {{mol.md30_std.toFixed(1)}} {{mol.md34_mean.toFixed(1)}} ± {{mol.md34_std.toFixed(1)}} {{mol.md37_mean.toFixed(1)}} ± {{mol.md37_std.toFixed(1)}} {{mol.md40_mean.toFixed(1)}} ± {{mol.md40_std.toFixed(1)}} {{mol.md50_mean.toFixed(1)}} ± {{mol.md50_std.toFixed(1)}} {{mol.md70_mean.toFixed(1)}} ± {{mol.md70_std.toFixed(1)}}

Result set is empty.
Empty boxes consider all items.
UID PDB Sequence Len Description Score Local % Global %
{{pdb}} +{{dna.PDBs.length-4}} {{dna.sequence.substring(0, 10) + '...' + dna.sequence.substring(dna.sequence.length-10, dna.sequence.length)}}
{{dna.sequence}}
{{dna.sequence.length}}
{{dna.auth_desc.substring(0, 20)+' ...'}}
{{dna.auth_desc}}
{{dna.Score}} {{dna.globalSim.toFixed(2)}} {{dna.localSim.toFixed(2)}}
{{dna.auth_desc}}
Organisms

{{o}}

Sequence {{dna.sequence.length}} nucleotides

{{dna.sequence}}

PDB IDs {{dna.PDBs.length}} PDB chains

{{pdb}}

Similairty Alignemnt Index
UID Score Local Global (Identical) Start End
{{sim.uid1}} {{sim.uid2}} {{sim.score}} {{sim.LocalSimilarity.toFixed(2)}} % {{sim.GlobalSimilarity.toFixed(2)}} % {{sim.start}} {{sim.end}}
Atoms' count closer than thresholds in Angstrom(Å)
Protein #Complexes 2.0 2.5 3.0 3.4 3.7 4.0 5.0 7.0
{{mol.uid_pro}} {{mol.frequency}} {{mol.md20_mean.toFixed(1)}} ± {{mol.md20_std.toFixed(1)}} {{mol.md25_mean.toFixed(1)}} ± {{mol.md25_std.toFixed(1)}} {{mol.md30_mean.toFixed(1)}} ± {{mol.md30_std.toFixed(1)}} {{mol.md34_mean.toFixed(1)}} ± {{mol.md34_std.toFixed(1)}} {{mol.md37_mean.toFixed(1)}} ± {{mol.md37_std.toFixed(1)}} {{mol.md40_mean.toFixed(1)}} ± {{mol.md40_std.toFixed(1)}} {{mol.md50_mean.toFixed(1)}} ± {{mol.md50_std.toFixed(1)}} {{mol.md70_mean.toFixed(1)}} ± {{mol.md70_std.toFixed(1)}}

Result set is empty.
Empty boxes consider all items.
UID PDB Sequence Len Description Score Local % Global %
{{pdb}} +{{protein.PDBs.length-4}} {{protein.sequence.substring(0, 10) + '...' + protein.sequence.substring(protein.sequence.length-10, protein.sequence.length)}}
{{protein.sequence}}
{{protein.sequence.length}}
{{protein.auth_desc.substring(0, 20)+' ...'}}
{{protein.auth_desc}}
{{protein.Score}} {{protein.globalSim.toFixed(2)}} {{protein.localSim.toFixed(2)}}
{{protein.auth_desc}}
Organisms

{{o}}

Sequence {{protein.sequence.length}} amino acids

{{protein.sequence}}

PDB IDs {{protein.PDBs.length}} PDB chains

{{pdb}}

Similairty Alignemnt Index
UID Score Local Global (Identical) Start End
{{sim.uid1}} {{sim.uid2}} {{sim.score}} {{sim.LocalSimilarity.toFixed(2)}} % {{sim.GlobalSimilarity.toFixed(2)}} % {{sim.start}} {{sim.end}}
Atoms' count closer than thresholds in Angstrom(Å)
RNA #Complexes 2.0 2.5 3.0 3.4 3.7 4.0 5.0 7.0
{{molr.uid_na}} {{molr.frequency}} {{molr.md20_mean.toFixed(1)}} ± {{molr.md20_std.toFixed(1)}} {{molr.md25_mean.toFixed(1)}} ± {{molr.md25_std.toFixed(1)}} {{molr.md30_mean.toFixed(1)}} ± {{molr.md30_std.toFixed(1)}} {{molr.md34_mean.toFixed(1)}} ± {{molr.md34_std.toFixed(1)}} {{molr.md37_mean.toFixed(1)}} ± {{molr.md37_std.toFixed(1)}} {{molr.md40_mean.toFixed(1)}} ± {{molr.md40_std.toFixed(1)}} {{molr.md50_mean.toFixed(1)}} ± {{molr.md50_std.toFixed(1)}} {{molr.md70_mean.toFixed(1)}} ± {{molr.md70_std.toFixed(1)}}
Atoms' count closer than thresholds in Angstrom(Å)
DNA #Complexes 2.0 2.5 3.0 3.4 3.7 4.0 5.0 7.0
{{mold.uid_na}} {{mold.frequency}} {{mold.md20_mean}} ± {{mold.md20_std}} {{mold.md25_mean}} ± {{mold.md25_std}} {{mold.md30_mean}} ± {{mold.md30_std}} {{mold.md34_mean}} ± {{mold.md34_std}} {{mold.md37_mean}} ± {{mold.md37_std}} {{mold.md40_mean}} ± {{mold.md40_std}} {{mold.md50_mean}} ± {{mold.md50_std}} {{mold.md70_mean}} ± {{mold.md70_std}}
Result set is empty.
{{ComplexResult.Message}}
UID Protein Nucleic Acid #Complex Distance(p,na) <= {{ ComplexResult.Tag['Distance']}} Å
{{comp.uid_pro}} {{comp.sequence_type}} | {{comp.uid_na}} {{comp.frequency}} {{comp[ComplexResult.Tag['FieldName']].toFixed(0)}}
Protein Description: {{comp.desc_protein}}
Protein PDBs: {{p}}
{{comp.sequence_type}} Description: {{comp.desc_na}}
{{comp.sequence_type}} PDBs: {{p}}
Cutoff Numeber of Atoms (all distances) Residues (Closest atoms) Residues (Centers' distance)
Å Min Median Max Avg Std
{{(parseFloat(d)/10).toFixed(1)}} {{comp['md'+d+pf].toFixed(1)}} {{comp['rm'+d+pf].toFixed(1)}} {{comp['rc'+d+pf].toFixed(1)}}
Protein Sequence: {{comp.seq_protein.length}} amino acids {{comp.seq_protein}}
{{comp.sequence_type}} Sequence: {{comp.seq_na.length}} nucleotides {{comp.seq_na}}
Accession Clan Name # Pfams # Interactive Pfams # Interacting Proteins
{{clan.CLAN_NAME}} {{clan.PfamNumber}} {{clan.InteractivePfamNumber}} {{clan.ProteinNumber}}
Pfam Accession Pfam Name Description Clan Accession # Interacting Proteins
{{pfam.PFAM_NAME}} {{pfam.Description}} {{pfam.CLAN_ACCESSION}} {{pfam.ProteinNumber}}
Click buttons to reload desired neighbors of the nodes added in the graph

{{Neighbor.SelectedNode.sequence_type}}: {{Neighbor.SelectedNode.uid}}
Interactions
{{pair.uid}}
Similar macromolecules
{{uid}} {{sim.GlobalSimilarity.toFixed(1)}}

The graph is empty

Open the dynamic representation of the graph in a new window
RNA: {{GraphInfo.NodeInfo.RNA}} DNA: {{GraphInfo.NodeInfo.DNA}} Protein: {{GraphInfo.NodeInfo.Protein}} Clan: {{GraphInfo.NodeInfo.Clan}} Pfam: {{GraphInfo.NodeInfo.PFAM}} Similarity: {{GraphInfo.EdgeInfo.Similarity}} Nucleic Acid Protein Binding: {{GraphInfo.EdgeInfo.NAProBinding}} Protein Pfam: {{GraphInfo.EdgeInfo.ProteinPfam}} Clan Pfam: {{GraphInfo.EdgeInfo.ClanPfam}} Connected Compoenents: {{GraphInfo.ConnectedComponents}}
D: DNA | R: RNA | PA: Protein | C: Clan | PF: Protein Family
NC: Not converged (limitations are depends on server resources and nodes` count)
Node Degree in subgraph Closeness Centrality Betweenness Centrality Eigenvector Centrality Degree in Total
{{gi.Node}} {{gi.SubgraphDegree}} {{(gi.ClosenessCentrality*100).toFixed(2)}}% {{(gi.BetweennessCentrality*100).toFixed(2)}}% {{(gi.EigenvectorCentrality*100).toFixed(2)}}% {{gi.EigenvectorCentrality}} {{gi.TotalDegree}}
Keywords in the graph
The Graph Components container is empty. Add some nodes first.
Graph Components
Preview - Total {{GCs.length}} items.
{{el.uid}}
Import to Graph Components
Export Network The Graph Components container is empty. Add some nodes first.
Dynamic representation Show The graph must be rebuilt first
The Graph Components container is empty. Add some nodes first.
{{cd.uid}} {{cd.type}} {{cd.title}} {{cd.description}}
{{cd.context}}
nematzadeh.sajjad@gmail.com